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HIV Study Tutorial
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Example1.xar.xml

I have installed CPAS 1.1 on Fedora Core 4. Using MS Internet Explorer, I am trying to load Example1.xar.xml on my project by clicking "Upload Experiment" under the Experiment tab. I have an error when doing that, so I click on the link "upload.xar.log" only to see this: 13 Jan 2006 15:56:29,211 INFO : Experiment Import for Uploaded file: 1/13/2006 15:56:29 13 Jan 2006 15:56:29,211 INFO : =======================================...

"log.txt" attached to message "Failure to see MS1 spectrum (or EIC) in CPAS website"

28 �@�� 2008 12:01:25,578 INFO : Mascot search for 1-1.mzXML 28 �@�� 2008 12:01:25,593 INFO : ======================================= 28 �@�� 2008 12:01:25,640 INFO : MzXML2Search output 28 �@�� 2008 12:01:25,640 INFO : ======================================= 28 �@�� 2008 12:02:02,203 INFO : running: MzXML2Search -mgf 1-1.mzXML 28 �@�� 2008 12:02:02,421 INFO : 28 �@�� 2008 12:02:02,421 INFO...

"QP01327ecn_mseclm.noinprevnext.calib.deconv.mgf.log" attached to message "Mascot searching"

20 maj 2008 13:26:15,186 INFO : Mascot search for QP01327ecn_mseclm.noinprevnext.calib.deconv.mgf 20 maj 2008 13:26:15,187 INFO : ======================================= 20 maj 2008 13:26:15,740 INFO : Check FASTA validity 20 maj 2008 13:26:15,775 INFO : ======================================= 20 maj 2008 13:26:15,848 INFO : 20 maj 2008 13:26:16,108 INFO : MzXML2Search output 20 maj 2008 13:26:16,108...

(1) Search of assay contant data (2) Hierarchy concept

(1) Search is not working for me.   https://www.labkey.org/wiki/home/Documentation/page.view?name=luceneSearch I used the above document to search to take out all assay runs and batches that contains a string “OTD*”. I checked all categories and scopes to make sure it will return the information but it wasn’t. Could you tell me why my search is not returning obvious data? (2) Hierarchy concept...

"CAexample_mini.log" attached to message "CPAS / Mascot Timeout"

01 Feb 2007 11:30:50,922 INFO : Mascot search for CAexample_mini.mzXML 01 Feb 2007 11:30:50,923 INFO : ======================================= 01 Feb 2007 11:30:50,996 INFO : MzXML2Search output 01 Feb 2007 11:30:50,996 INFO : ======================================= 01 Feb 2007 11:30:51,039 INFO : running: MzXML2Search -mgf CAexample_mini.mzXML 01 Feb 2007 11:30:51,259 INFO : 01 Feb 2007 11:30:51,259...

"KRL01-092906-TZ-0145-GEL-FT-01.log" attached to message "Is it X! tendem parameter error or other permission error?"

18 Nov 2006 06:30:39,843 INFO : X! Tandem search for KRL01-092906-TZ-0145-GEL-FT-01.mzXML 18 Nov 2006 06:30:39,848 INFO : ======================================= 18 Nov 2006 06:30:39,898 INFO : tandem.exe output 18 Nov 2006 06:30:39,901 INFO : ======================================= 18 Nov 2006 06:30:39,907 INFO : running: tandem.exe input.xml 18 Nov 2006 06:30:40,098 INFO : 18 Nov 2006 06:30:40,102...

Set Up Docker with TLS

Premium Feature — Docker supports rstudio, which is part of the Professional and Enterprise Editions of LabKey Server. Learn more or contact LabKey for details. This topic outlines an example TLS and certificate configuration used to set up Docker for use with RStudio in LabKey Server. The main instructions for configuring Docker and RStudio are in this topic: docker Installation Instructions...

Failed runing xinteract

Hi all, I have checked the term of "Failed running xinteract" in this forum, but no good answer can solve my problem. I run Mascot (version 2.1)search in the CPAS in my WinXP SP2 desktop. Most of mzXML worked successfully but few of them can not work and showed the error message as below 16 一月 2008 23:25:58,221 INFO : Mascot search for 4-11.mzXML 16 一月 2008 23:25:58,221 INFO : =======================================...

"SmallICAT.log" attached to message "ERROR: Failed to delete SmallICAT.work"

19 Jun 2006 18:27:31,013 INFO : X! Tandem search for SmallICAT.mzXML 19 Jun 2006 18:27:31,015 INFO : ======================================= 19 Jun 2006 18:27:31,106 INFO : tandem.exe output 19 Jun 2006 18:27:31,111 INFO : ======================================= 19 Jun 2006 18:27:31,113 INFO : running: tandem.exe input.xml 19 Jun 2006 18:27:31,154 INFO : 19 Jun 2006 18:27:31,155 INFO : X! TANDEM...

Configuration error deteced at LabKey Server Startup

Hello,   I am trying to install a local LabKey server on a machine running CentOS 6. I went through the installation steps, but am receiving this error when I go to open labkey in my browser. Also, I am only able to start up postgres when I am logged in as root; does this have something to do with the error? I am relatively new to Linux so please bear with me.   org.labkey.api.util.ConfigurationException:...

Creating New Modules

Hi guys, Wondering if I can get any guidance on coding my own module. I've compiled 1.4 from source code, tinkered with the demo module, and taken a look at the build scripts. As a first step, I copied the demo module into another directory in the modules folder and modified the build script: added <antcall target="myModule"/> to "build_module_classes" target 2. added   <target name="myModule"...

"QuerySnapshotCreationError.txt" attached to message "Cannot create query snapshot with large number of columns in 14.1"

500: Unexpected server error SqlExecutor.execute(); SQL []; ERROR: functions cannot have more than 100 arguments; nested exception is org.postgresql.util.PSQLException: ERROR: functions cannot have more than 100 arguments org.springframework.dao.DataAccessResourceFailureException: SqlExecutor.execute(); SQL []; ERROR: functions cannot have more than 100 arguments; nested exception is org.postgresql.util.PSQLException:...

lin_384_well_metadata.xls

data SampleWellGroup PlateLocation SpecimenID ParticipantID VisitID Date SampleDescription Lot Number InitialDilution Factor Method Specimen 1 A3-A4 4E10 Antibody Lot 1 10 3 Concentration Specimen 2 B3-B4 2F5 Antibody Lot 1 10 3 Concentration Specimen 3 C3-C4 2G12 Antibody Lot 1 10 3 Concentration Specimen 4 D3-D4 sCD4 Antibody Lot 1 10 3 Concentration Specimen 5 E3-E4 HIVIG Antibody...

Error when upgrading

I'm trying to upgrade our prod Labkey docker instance from 23.3.2 to 23.11.11. The upgrade went ok on our dev instance but the upgrade fails every time when we try on prod, leaving things in a broken state so we have to roll back the database. I've done the database check via the UI and no issues are found. The issue seems to be related to the Experiment module : INFO ModuleLoader ...

"PepcPipeline.log" attached to message "Runtime error when queueing pipelinejob"

12 Sep 2008 10:06:27,512 ERROR: Failed to set status to 'WAITING' for 'PepcPipeline.status'. com.thoughtworks.xstream.converters.reflection.ObjectAccessException: Could not get field class java.lang.reflect.Field.name : Can not set java.lang.String field org.apache.commons.logging.impl.Log4JLogger.name to org.apache.commons.logging.impl.Log4JLogger at com.thoughtworks.xstream.converters.reflection.PureJavaReflectionProvider.visitSerializableFields(PureJavaReflectionProvider.java:111)...

Is it X! tendem parameter error or other permission error?

I was trying to non-specific cleavage search with X! tendem parameters [X][X]. I got the following error messages. 17 Nov 2006 15:09:44,094 INFO : command "PeptideProphetParser DSL02-081406-TZ-0199-GEL-FT-01.pep.xml MINPROB=0" exited with non-zero exit code: 256 17 Nov 2006 15:09:44,096 INFO : QUIT - the job is incomplete 17 Nov 2006 15:09:44,117 ERROR: Failed to move /proteomics/Duffy/CPASPiplineRoot...

"getContainers-atlas-test.txt" attached to message "Strange behavior with LABKEY.Security.getContainers() function"

https://atlas-test.scharp.org/cpas/project/HVTN/Specimen%20Management/Lab%20Program/begin.view? https://atlas-test.scharp.org/cpas/project/HVTN/getContainers.view?_dc=1348616911600&container=%2FHVTN%2FSpecimen%20Management%2FLab%20Program%2F&includeSubfolders=false _dc=1348616911600 container=/HVTN/Specimen Management/Lab Program/ includeSubfolders=false { "sortOrder": 0, "children": [...

"labkey.log" attached to message "Error while running trigger script"

INFO ScriptService$Console 2020-04-07 17:59:07,547 io-127.0.0.1-8080-exec-4 : ** evaluating: queries/study/BasicsCase.js INFO ScriptService$Console 2020-04-07 17:59:07,584 io-127.0.0.1-8080-exec-4 : Getting entries in BasicsCase, success: 33 rows returned. INFO ScriptService$Console 2020-04-07 17:59:07,584 io-127.0.0.1-8080-exec-4 : Selected rows BasicsCase: INFO ScriptService$Console...

Luminex_Assay_200-2015-06-09-1221.tsv

container date wellRole fiBackgroundNegative stdCurve fiOORIndicator specimenID type singlePointControl excluded samplingErrors protocol regressionType outlier resVar fiBackground fiBackgroundString dilution name extraSpecimenInfo stdDevOORIndicator expConc stdDev maxStandardRecovery obsConc fi obsConcOORIndicator minStandardRecovery obsConcString beadCount description lsid dataId fiString obsOverExp...

"catalina.out" attached to message "server crashing"

Feb 16, 2010 2:11:16 PM org.apache.catalina.core.AprLifecycleListener lifecycleEvent INFO: The Apache Tomcat Native library which allows optimal performance in production environments was not found on the java.library.path: /usr/java/jdk1.6.0_14/jre/lib/amd64/server:/usr/java/jdk1.6.0_14/jre/lib/amd64:/usr/java/jdk1.6.0_14/jre/../lib/amd64:/usr/java/packages/lib/amd64:/lib:/usr/lib Feb 16, 2010 2:11:16...